timeseries_clustering_flu.py

"""
Created on 11 Apr 2019

@author: jhkwakkel
"""

import matplotlib.pyplot as plt
import seaborn as sns

from ema_workbench import load_results
from ema_workbench.analysis import clusterer, plotting, Density

experiments, outcomes = load_results("./data/1000 flu cases no policy.tar.gz")
data = outcomes["infected_fraction_R1"]

# calculate distances
distances = clusterer.calculate_cid(data)

# plot dedrog
clusterer.plot_dendrogram(distances)

# do agglomerative clustering on the distances
clusters = clusterer.apply_agglomerative_clustering(distances, n_clusters=5)

# show the clusters in the output space
x = experiments.copy()
x["clusters"] = clusters.astype("object")
plotting.lines(x, outcomes, group_by="clusters", density=Density.BOXPLOT)

# show the input space
sns.pairplot(
    x,
    hue="clusters",
    vars=[
        "infection ratio region 1",
        "root contact rate region 1",
        "normal contact rate region 1",
        "recovery time region 1",
        "permanent immune population fraction R1",
    ],
    plot_kws=dict(s=7),
)
plt.show()